Alignments for a candidate for kbl in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for kbl in Stenotrophomonas chelatiphaga DSM 21508

Align glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate WP_057507008.1 ABB28_RS02025 glycine C-acetyltransferase

Query= BRENDA::P0AB77
         (398 letters)



>NCBI__GCF_001431535.1:WP_057507008.1
          Length = 400

 Score =  512 bits (1318), Expect = e-150
 Identities = 260/388 (67%), Positives = 305/388 (78%)

Query: 10  TNDLETARAEGLFKEERIITSAQQADITVADGSHVINFCANNYLGLANHPDLIAAAKAGM 69
           T +L+  RA+GLFK ERIITS Q A+IT+ DG  V+NFCANNYLGLA+HPDLI AAK  +
Sbjct: 13  TEELDAIRAQGLFKSERIITSPQSAEITLEDGRTVLNFCANNYLGLADHPDLIQAAKDAL 72

Query: 70  DSHGFGMASVRFICGTQDSHKELEQKLAAFLGMEDAILYSSCFDANGGLFETLLGAEDAI 129
           DSHGFGMASVRFICGTQD HK+LE ++A F G +D ILY++CFDANGGLFE LLG +DAI
Sbjct: 73  DSHGFGMASVRFICGTQDLHKQLEAQIAGFFGKQDTILYAACFDANGGLFEPLLGEQDAI 132

Query: 130 ISDALNHASIIDGVRLCKAKRYRYANNDMQELEARLKEAREAGARHVLIATDGVFSMDGV 189
           ISD+LNHASIIDGVRLCKAKR+RYAN DM +LEA+L+ A  AG R  LI TDGVFSMDG 
Sbjct: 133 ISDSLNHASIIDGVRLCKAKRFRYANCDMADLEAQLQAADAAGCRTKLITTDGVFSMDGF 192

Query: 190 IANLKGVCDLADKYDALVMVDDSHAVGFVGENGRGSHEYCDVMGRVDIITGTLGKALGGA 249
           IA L  +  LA KY ALV +D+ HA GF+G  GRGS E   V+ ++DIITGTLGKA+GGA
Sbjct: 193 IAPLDEITALAQKYGALVHIDECHATGFLGATGRGSAEVKGVLEKIDIITGTLGKAMGGA 252

Query: 250 SGGYTAARKEVVEWLRQRSRPYLFSNSLAPAIVAASIKVLEMVEAGSELRDRLWANARQF 309
            GG+T A+ EV+E LRQRSRPYLFSNSL P +VAA IK  EM+ A  +LR  L AN   F
Sbjct: 253 LGGFTTAKAEVIELLRQRSRPYLFSNSLPPHVVAAGIKAFEMLAAADDLRGTLVANTTYF 312

Query: 310 REQMSAAGFTLAGADHAIIPVMLGDAVVAQKFARELQKEGIYVTGFFYPVVPKGQARIRT 369
           RE+M AAGF +    H I PVML DA +AQKFA  L +EGIY  GFF+PVVPKGQARIRT
Sbjct: 313 REKMVAAGFDVKPGVHPISPVMLYDAPLAQKFAERLLEEGIYAIGFFFPVVPKGQARIRT 372

Query: 370 QMSAAHTPEQITRAVEAFTRIGKQLGVI 397
           Q+SAAHT E + RA++AFTRIG++LGVI
Sbjct: 373 QISAAHTREHLDRAIDAFTRIGRELGVI 400


Lambda     K      H
   0.320    0.135    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 496
Number of extensions: 16
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 398
Length of database: 400
Length adjustment: 31
Effective length of query: 367
Effective length of database: 369
Effective search space:   135423
Effective search space used:   135423
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate WP_057507008.1 ABB28_RS02025 (glycine C-acetyltransferase)
to HMM TIGR01822 (kbl: glycine C-acetyltransferase (EC 2.3.1.29))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01822.hmm
# target sequence database:        /tmp/gapView.3620.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01822  [M=393]
Accession:   TIGR01822
Description: 2am3keto_CoA: glycine C-acetyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.6e-226  736.4   0.7     4e-226  736.2   0.7    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057507008.1  ABB28_RS02025 glycine C-acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057507008.1  ABB28_RS02025 glycine C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.2   0.7    4e-226    4e-226       2     393 .]       9     400 .]       8     400 .] 1.00

  Alignments for each domain:
  == domain 1  score: 736.2 bits;  conditional E-value: 4e-226
                                 TIGR01822   2 kailaaelesireaGlfkkeriitspqkadirvadGrevlnfcannylGlsdhpeviqaakdaldehGf 70 
                                               + +++ el++ir++Glfk+eriitspq+a+i++ dGr vlnfcannylGl+dhp++iqaakdald+hGf
  lcl|NCBI__GCF_001431535.1:WP_057507008.1   9 TRHYTEELDAIRAQGLFKSERIITSPQSAEITLEDGRTVLNFCANNYLGLADHPDLIQAAKDALDSHGF 77 
                                               67899**************************************************************** PP

                                 TIGR01822  71 GlssvrficGtqdlhkelekklaeflgtedailyascfdangGlfeallgeedaiisdalnhasiidGv 139
                                               G++svrficGtqdlhk+le+++a f+g++d+ilya+cfdangGlfe+llge+daiisd+lnhasiidGv
  lcl|NCBI__GCF_001431535.1:WP_057507008.1  78 GMASVRFICGTQDLHKQLEAQIAGFFGKQDTILYAACFDANGGLFEPLLGEQDAIISDSLNHASIIDGV 146
                                               ********************************************************************* PP

                                 TIGR01822 140 rlckakryryenadledleaklkearaagarlrliatdGvfsmdGtiapldeicalaekydalvlvdec 208
                                               rlckakr+ry+n+d++dlea+l++a+aag+r++li+tdGvfsmdG+iapldei+ala+ky+alv++dec
  lcl|NCBI__GCF_001431535.1:WP_057507008.1 147 RLCKAKRFRYANCDMADLEAQLQAADAAGCRTKLITTDGVFSMDGFIAPLDEITALAQKYGALVHIDEC 215
                                               ********************************************************************* PP

                                 TIGR01822 209 hatGflGatGrGsaelldvldkvdiitgtlGkalGGasGGfttakkevvellrqrsrpylfsnslapav 277
                                               hatGflGatGrGsae+++vl+k+diitgtlGka+GGa+GGfttak ev+ellrqrsrpylfsnsl+p+v
  lcl|NCBI__GCF_001431535.1:WP_057507008.1 216 HATGFLGATGRGSAEVKGVLEKIDIITGTLGKAMGGALGGFTTAKAEVIELLRQRSRPYLFSNSLPPHV 284
                                               ********************************************************************* PP

                                 TIGR01822 278 vgasikvlelleasnelrdklventryfrekleaaGfdvkpaehaiipvmlydaklaqklaerlleeGi 346
                                               v+a+ik++e+l a+++lr  lv+nt yfrek+ aaGfdvkp+ h+i+pvmlyda laqk+aerlleeGi
  lcl|NCBI__GCF_001431535.1:WP_057507008.1 285 VAAGIKAFEMLAAADDLRGTLVANTTYFREKMVAAGFDVKPGVHPISPVMLYDAPLAQKFAERLLEEGI 353
                                               ********************************************************************* PP

                                 TIGR01822 347 yviGffypvvpkGqarirvqlsaaheeeqldkaveafvkvGrelgvi 393
                                               y+iGff+pvvpkGqarir+q+saah++e+ld+a++af+++Grelgvi
  lcl|NCBI__GCF_001431535.1:WP_057507008.1 354 YAIGFFFPVVPKGQARIRTQISAAHTREHLDRAIDAFTRIGRELGVI 400
                                               *********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (393 nodes)
Target sequences:                          1  (400 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.72
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources